Biology subjects

Bernard, C.

Publications and source records attributed to Bernard, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Microdiversity drives resilience and niche partitioning in the bloom forming cyanobacteria Limnospira platensis

The intraspecific evolutionary mechanisms of adaptation in blooming cyanobacteria, particularly those occurring on small spatial and temporal scales, remain poorly understood. Here, we used the unique properties of Lake Dziani Dzaha, which hosts a persistent population of Limnospira platensis inhabiting distinct macro-habitats, to explore the spatial and temporal dynamics of microevolution. The Lake Dziani Dzaha (Mayotte), very stable at least since 2010, has experienced a seismo-volcanic crisis from May 2018 to November 2019, characterized by CO2 outgassing that led to the mixing of the initially seasonally stratified water column, as well as changes in numerous physicochemical parameters. Phylogenomic analysis of 108 strains isolated during sampling campaigns in 2010, 2014, 2022, and 2024 revealed a population that remained highly phylogenetically cohesive over time. In 2022, genomic expansion was observed, characterized by an increase in genome size due to the proliferation of insertion sequences and a subsequent loss of adaptive genes. By 2024, a rapid recovery of the 2010-2014 genetic content took place through multiple independent events of horizontal gene transfer. At the spatial scale, although no significant differences in gene content were detected, distinct subpopulations were identified based on allele frequencies. Some alleles were specifically fixed and subject to different selection pressures among the subpopulations, suggesting the existence of distinct ecotypes. Overall, this study highlights the role of microdiversity in rapid resilience of blooming cyanobacteria populations within dynamic environments and in their adaptation through niche partitioning.

microbiology↗

bioRxiv2026

The influence of nutrient enrichment and fish addition on microbial communities in water and fish guts during mesocosm experiments conducted in a tropical freshwater lagoon (Lagoon Aghien, Cote dIvoire)

Freshwater ecosystems in the intertropical zone have received considerably less scientific attention than those in temperate regions, with the notable exception of a few large and iconic lakes, such as Lake Victoria. Consequently, the diversity, functioning, and pollution sensitivity of microbial communities in these systems remain poorly understood. To investigate the short-term responses of microbial communities to nutrient enrichment and fish addition, we conducted in situ mesocosm experiments at two stations in a freshwater lagoon near Abidjan (Cote dIvoire). Phosphorus enrichment, either alone or in combination with nitrogen, led to a consistent increase in bacterial abundance across mesocosms, suggesting a potential phosphorus limitation of bacterial growth by these nutrients and consequently a potential competition for this resource between bacteria and microphytoplankton. In contrast, picophytoplankton abundances showed no clear or consistent response to nutrient enrichment, suggesting that other ecological processes may play a more important role in regulating these communities. High-throughput Illumina sequencing revealed contrasting patterns in the relative abundance of cyanobacterial and chloroplast-associated reads, depending on both nutrient enrichment and fish addition. These results, consistent with those obtained by cell counting in a previous study, suggest a potential top-down control of cyanobacteria by fish in Lagoon Aghien. In addition, nutrient (phosphorus and nitrogen combined) enrichment and fish addition significantly affected the amplicon sequence variant (ASV) composition of bacterial communities. Overall, these findings provide new insights into the drivers shaping microbial community structure in tropical freshwater ecosystems and are discussed in the context of previously published data on phytoplankton dynamics from the same experimental system.

ecology↗

bioRxiv2026

The Internal Structure of Seizures Reflects Animal-Specific Trajectories of Disease Progression and Circadian Modulation in Epileptic Mice

Epileptic seizures arise from the abnormal, sustained recruitment of neuronal populations, yet the temporal organisation of activity within individual seizures remains poorly understood. We hypothesised that seizures follow structured trajectories through a restricted state space rather than random patterns of activity. To test this idea, we analysed continuous long-term EEG recordings from six mice with pilocarpine-induced temporal lobe epilepsy and developed a symbolic framework that transforms seizure activity into sequences of discrete burst states. Across more than one thousand spontaneous seizures, we found that seizures are organised by sparse, animal-specific transition rules linking a small repertoire of recurrent burst motifs. These rules evolve over the course of epilepsy: early seizures display substantial variability in burst composition, and, to a smaller but statistically significant degree, in transition structure, whereas later seizures become more stereotyped in which burst types they use, a pattern suggestive of consolidation of the epileptic network into a stable dynamical regime. Seizure microstructure was further modulated by circadian phase, indicating that biological rhythms influence not only when seizures occur but also how they unfold. Moreover, burst sequences exhibited higher-order temporal dependencies that could not be explained by first-order Markov statistics alone. Together, these results reveal an evolving seizure grammar that links ictal dynamics to disease progression and circadian regulation, establishing symbolic dynamics as a powerful framework for quantifying the internal organisation of seizures.

neuroscience↗

bioRxiv2026

The CNS-penetrant MAP4K inhibitor famlasertib restrains medulloblastoma dissemination without developmental toxicity

Cerebellum tissue invasion and dissemination are major drivers of recurrence and metastatic spread in medulloblastoma (MB), yet no invasion-inhibitory therapy is currently available. The serine/threonine kinase MAP4K4 is highly expressed in MB and promotes invasive behavior downstream of growth factor signaling, while its physiological postnatal downregulation suggests that disrupted developmental control may contribute to tumor pathogenesis. Here, we investigate pharmacological targeting of MAP4K4 using famlasertib, a CNS-penetrant, neuroprotective MAP4K inhibitor, as a strategy to suppress invasion in MB. Using 3D invasion assays and quantitative live-cell microscopy, we demonstrate that famlasertib markedly reduces invasive behavior and single-cell motility of MB cells. Organotypic cerebellum tissue and orthotopically implanted zebrafish larval models further confirm anti-invasive efficacy without detectable developmental toxicity at effective concentrations. Phospho-proteomics and functional analyses revealed that MAP4K inhibition alters kinase signaling linked to cytoskeletal remodeling, leading to suppressed F-actin dynamics, increased cell clustering, and enhanced cortical accumulation of tight junction protein 1 (TJP1). Collectively, our findings confirm MAP4Ks as therapeutically targetable regulators of MB invasion and establish famlasertib as a candidate migrastatic agent that restrains tumor cell dissemination while preserving developmental integrity.

cancer biology↗

bioRxiv2025

Higher trophic status leads to more diverse and divergent microeukaryote communities over time in urban lakes from the Greater Paris (France)

Effects of trophic status on lake microeukaryote community dynamics remain underexplored. Spanning oligotrophic to hypereutrophic conditions, peri-urban lakes located in the Greater Paris region (France) offer unique opportunities to compare these dynamics along a eutrophication gradient. Here, community composition was characterized using 18S rRNA gene metabarcoding, and analyzed in the context of environmental parameters and chlorophyll a-derived trophic status throughout an 18-month sampling period. Microeukaryote assemblages were dominated by Cryptophyceae, Spirotrichea, Chrysophyceae, and Chlorophyceae, with mixotrophic and heterotrophic taxa dominating across all lakes. Taxa richness peaked at intermediate trophic levels, consistent with the intermediate disturbance hypothesis. Beta-diversity and network analyses revealed increasing community modularity, reduced connectivity, and enhanced temporal variability with higher trophic status. In lakes reaching the hypereutrophic status, communities diverged progressively over time, suggesting the onset of regime shifts. Conversely, oligo-to mesotrophic lakes maintained more connected and stable assemblages. These findings demonstrate that eutrophication fosters more diverse and increasingly divergent microeukaryote communities, underscoring its role as a central driver of microbial community restructuring in urban freshwater systems.

microbiology↗

bioRxiv2025

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community

Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolutionary question in an open marine animal associated system, through two longitudinal samplings years apart in an oyster farm, obtaining >1,000 virulent phages and >600 Vibrio crassostreae strains. Surprisingly, lineages of phage and bacteria were very persistent, with some phages remaining strictly identical after four years. The phage-vibrio infection network remained modular with multiple lineages co-habitating within individual oysters for long periods of time. Seasonal restriction of V. crassostreae, overwintering in wild oysters, and limited viral decay may explain phage stability. Oysters also act as hotspots of activity of diverse mobile genetic element (MGE), hosting plasmids, prophages, phage-plasmids and entirely new classes of satellite-plasmids. Our findings demonstrate how nested ecological constraints can stabilize viral lineages: oysters house vibrio populations that escape host immunity, vibrios restrict phages via receptors and defenses, and satellites parasitize their cognate helper phages. We suggest that ecological context can favor the long-term maintenance of viral lineages and stabilize MGE persistence in the ocean, even amid ongoing mutation and antagonistic co-evolution.

microbiology↗

bioRxiv2025

Data-driven Sampling Strategies for Fine-Tuning Bird Detection Models

Passive Acoustic Monitoring has emerged as a promising tool for collecting ecological data, particularly in the context of bird population monitoring. Bird species can be automatically identified using pre-trained models, such as BirdNET. The performance of these models can be significantly improved through fine-tuning with annotated samples recorded in the specific acoustic conditions in which the microphones are deployed. However, PAM collects vast amounts of data, and annotating bird vocalizations requires specialized expetise. As a result, only a very small portion of the recordings can be effectively labeled. Selecting the most relevant samples to annotate in order to maximize performance in model fine-tuning remains a significant challenge. First, a regularization technique addresses the challenge of class imbalance during model fine-tuning. Next, a data-driven methodology is developed, introducing the influence score, which quantifies the impact of individual training samples on model performance to inform sampling strategies. A linear model is proposed to estimate the influence score for generalization to unseen data. Finally, several sampling strategies are compared, based on acoustic indices and predictions of the pre-trained model. Together, these contributions enable the identification of efficient annotation strategies to overcome the challenges of limited annotation resources in large-scale passive acoustic monitoring.

bioinformatics↗

bioRxiv2025

Stratified Active Learning for Spatiotemporal Generalisation in Large-Scale Bioacoustic Monitoring

Active learning optimises machine learning model training through the data-efficient selection of informative samples for annotation and training. In the context of biodiversity monitoring using passive acoustic monitoring, active learning offers a promising strategy to reduce the fundamental annotation bottleneck and improve global training efficiency. However, the generalisability of model performance across ecologically relevant strata (e.g. sites, season etc) is often overlooked. As passive acoustic monitoring is extended to larger scales and finer resolutions, inter-strata spatiotemporal variability also increases. We introduce and investigate the concept of stratified active learning to achieve reliable and generalisable model performance across deployment conditions. We compare between implicit cluster-based diversification methods and explicit stratification, demonstrating that cross-strata generalisation is a function of stratum divergence, not sampling balance. Additionally, mutual information as well as exclusion analysis show that spatiotemporal context can explain a substantial proportion of species label variance and inform sampling decisions.

bioinformatics↗

bioRxiv2025

RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics

RNA is a molecule that performs critical roles in cellular biology, with its function closely dependent on its three-dimensional conformation. Predicting and evaluating RNA 3D structures remains a significant challenge in the field. Although many metrics and scoring functions have been developed to assess structural quality, each offers a different perspective, and no single method has emerged as a definitive standard. To address this, we previously introduced RNAdvisor, a comprehensive and automated software platform to evaluate 3D RNA structures using a wide range of existing quality metrics and scoring functions. This work presents RNAdvisor2, an extended and improved version of the tool. RNAdvisor 2 introduces a web server designed to enhance accessibility and usability for the broader research community. This release includes new scoring functions and integrates the novel concepts of meta-metrics and meta-scoring functions, which unify diverse evaluation criteria into more robust indicators of RNA structure quality. Additionally, the command-line tool has been improved and optimized for greater stability and extensibility, supporting scalable and maintainable future development. The web server, tool and its source code are freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.

bioinformatics↗

bioRxiv2025

Degeneracy and bifurcation diversity at the single neuron level

Degeneracy--the capacity of structurally distinct systems to achieve similar functions--is a fundamental property of living organisms, enabling adaptability and resilience. Neurons can maintain stable activity patterns despite wide variability in ion channel expression, highlighting how distinct internal configurations can yield equivalent electrophysiological behaviors. However, it remains unclear how degeneracy manifests in the context of bifurcations, the critical transitions between activity regimes that underlie phenomena such as different firing patterns, seizures and depolarization block. Here, we investigate how different biophysical parameter sets can lead to equivalent bifurcation sequences. Using a minimal neuron model with three variable conductances, we systematically explore how changes in extracellular potassium--mimicking physiological and pathological conditions--affect neuronal dynamics. Our results reveal that neurons with distinct intrinsic properties can traverse the same bifurcation pathways, entering regimes of bursting, seizure-like activity, and depolarization block. Yet, the specific parameter set determines the sensitivity and thresholds for these transitions. This work clarifies how degeneracy extends to the dynamical landscape of neurons, with implications for understanding resilience and vulnerability in neural circuits. 1 Author SummaryBiophysical models expressed through differential equations can reproduce the dynamics of biological systems with varying levels of detail. By changing model parameters, simulations can capture the natural variability that allows biological systems to achieve the same behavior through different mechanisms. This property, called degeneracy, underlies the robustness of living systems to internal and external perturbations. In this work, we identify dis-tinct behaviors in single-neuron models and link them to electrophysiological patterns observed under elevated extracellular potassium during epileptic events. These patterns correspond to specific classes of spontaneous bursting activity within the framework of nonlinear dynamics. We show that different combinations of conductance parameters, at a fixed extracellular potassium level, can generate the same class of patterns, defining degeneracy groups. Finally, we assess the robustness of these groups by analyzing how they respond to changes in extracellular potassium. Our findings provide a basis for studying variability and resilience in the dynamics of more complex neuronal systems.

neuroscience↗

bioRxiv2025

First detection of Crimean Congo Hemorrhagic Fever antibodies in cattle and wild fauna of southern continental France: investigation of explicative factors

Crimean-Congo Haemorrhagic Fever (CCHF) is a tick-borne zoonosis with significant public health implications due to its expanding geographic distribution and potential for severe outcomes in humans. This study represents the first serological survey conducted in mainland France to detect antibodies against the Crimean-Congo Haemorrhagic Fever Virus (CCHFV) in domestic and wild fauna, providing critical insights into the viruss circulation. We analyzed 8,609 cattle sera and 2,182 wildlife sera collected across the French Mediterranean region from 2008 to 2022, using enzyme-linked immunosorbent assays (ELISA) and pseudo-plaque reduction neutralization tests (PPRNT) for antibody detection and confirmation. Seropositivity was detected in both cattle (2.04%) and wildlife (2.25%), with higher rates observed in specific regions such as Pyrenees-Orientales and Hautes-Pyrenees. These findings reveal spatial clusters of CCHFV circulation and suggest the existence of enzootic transmission cycles involving local tick vectors and animal hosts. Our multivariate analysis identified key factors influencing seropositivity, including animal age, habitat characteristics, and potential wildlife interactions. The presence of natural open habitats and coniferous forests was significantly associated with higher seropositivity in cattle, while sex and geographical variability played a role in wildlife seroprevalence. These findings highlight the importance of environmental and anthropogenic factors in shaping the dynamics of CCHFV transmission. This study demonstrates that CCHFV is actively circulating in parts of mainland France, emphasizing the need for enhanced surveillance and integrated approaches to monitor zoonotic pathogens. It also raises questions about the role of additional tick vectors, such as Hyalomma lusitanicum, in the transmission cycle. These results contribute to a better understanding of CCHF epidemiology and offer valuable guidance for public health strategies to mitigate the risks associated with this emerging disease. Author SummaryCrimean-Congo Haemorrhagic Fever (CCHF) is a severe disease spread by ticks that affects humans and animals. Although the disease is largely distributed in parts of Europe, Africa, and Asia, its presence in France has been uncertain. My study investigated whether the virus causing this disease is circulating in southern mainland France by testing blood samples from domestic animals, like cattle, and wild animals, such as deer and wild boars, for signs of previous infection. I found evidence of the virus in several regions, particularly in the Pyrenees-Orientales, Hautes-Pyrenees and Alpes-maritimes, suggesting that the virus is indeed circulating among animals and ticks in some parts of mainland France. By studying where infected animals were found and considering factors such as age, habitat, and environmental conditions, I identified that older animals seem to have been more often exposed to the virus, as well as animals frequenting open environments favorable to ticks. These findings are important because they show that the disease could potentially spread to new areas and affect human populations. My work highlights the need for ongoing monitoring of ticks and animals for CCHFV epidemiological surveillance and the protection of public health.

ecology↗

bioRxiv2025

Persistent virulent phages exist in bacterial isolates

Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial cells through lysogeny. Virulent phages, characterized by their obligatory lytic cycle, are assumed to lack the ability to persist within bacterial colonies, and their infection is expected to decimate the host population under in-vitro conditions. Consequently, when bacterial isolates are cultured for sequencing, the resulting assemblies are not expected to contain virulent phage genomes. To test this assumption on a large scale, we analyzed over 267,000 publicly available Escherichia assemblies. Surprisingly, we identified 373 genomes corresponding to virulent phages within the bacterial genomes. These viral genomes are associated with specific phage groups and especially with jumbo phages with very large genomes (>200 kb). Chimallin was a core gene in two of these jumbo phage clusters, the major protein used by some jumbo phages to form a protective phage nucleus during infection. We found multiple lines of evidence suggesting that these virulent phage genomes in bacterial assemblies arise from persistent infections rather than contamination. Supporting this, we experimentally demonstrated the coexistence of non-temperate jumbo phages with their bacterial hosts. In a targeted follow-up search for three clades of persistent jumbo phages, we identified 285 additional jumbo phage genomes in bacterial taxa beyond Escherichia, highlighting that there are many more undiscovered persistent phages in bacterial assemblies. Our findings challenge the traditional virulent-temperate dichotomy, highlighting the overlooked diversity and prevalence of non-canonical phage lifestyles.

microbiology↗

bioRxiv2024

Generalists in a Specialist World: Vibrio-Phages with Broad Host Range

The host range of a bacteriophage--the diversity of hosts it can infect--is central to understanding phage ecology and applications. While most well-characterized phages have narrow host ranges, broad-host-range phages represent an intriguing component of marine ecosystems. The genetic and evolutionary mechanisms driving their generalism remain poorly understood. In this study, we analyzed Schizotequatroviruses and their Vibrio crassostreae hosts, collected from an oyster farm. Schizotequatroviruses exhibit broad host ranges, large genomes (~252 kbp) encoding 26 tRNAs, and conserved genomic organization interspersed with recombination hotspots. These recombination events, particularly in regions encoding receptor-binding proteins and antidefense systems, highlight their adaptability to host resistance. Notably, some lineages demonstrated receptor-switching between OmpK and LamB, showcasing their evolutionary flexibility. Despite their broad host range, Schizotequatroviruses were rare in the environment. Their scarcity could not be attributed to burst size, which was comparable to other phages in vitro, but may result from ecological constraints or fitness trade-offs, such as their preference for targeting generalist vibrios in seawater rather than the patho-phylotypes selected in oyster farms. Our findings clarify the genetic and ecological trade-offs shaping Schizotequatrovirus generalism and provide a foundation for future phage applications in aquaculture and beyond.

microbiology↗

bioRxiv2024

Intraspecific differences in alkaline tolerance in brook stickleback (Culaea inconstans) inhabiting neutral and alkaline lakes

Exposure to alkaline water (pH > 9.0) is physiologically challenging for fish, yet our understanding of the physiology of alkaline tolerance in fishes is limited to a small number of ihighly specialized species. This study aimed to characterize mechanisms of alkaline tolerance in brook stickleback (Culaea inconstans), a fish species with a broad pH habitat range, including highly alkaline waters such as Buffalo Lake (pH = 9.2) in Alberta, Canada. Stickleback from Buffalo Lake and a neutral reference lake (Buck Lake; pH = 8.2) were collected from the wild and acclimated to common conditions (pH = 8.0) for at least 2 months. Both populations were then exposed to alkaline conditions (pH = 9.5), resulting in a significant decrease in survival (14% by 7 d of exposure) in Buck Lake fish, but no mortality in Buffalo Lake stickleback. In a 4-d exposure to alkaline water, fish from both populations experienced characteristic inhibitions of ammonia excretion followed by subsequent recovery, in conjunction with an accumulation of ammonia within the body. However, no differences were observed between populations. Analysis of tissue Na+ and Cl- content showed a more pronounced decrease in Cl- in Buck Lake fish, suggesting that tighter regulation of Cl- homeostasis and/or acid-base balance may be an important feature of alkaline tolerance. RNA-sequencing analysis highlighted large differences in gene expression between the alkaline and neutral lake populations, and in response to alkaline exposure. Few of these changes in the expression involved genes known to be associated with nitrogen, ion, or acid-base balance. These data indicate that alkaline tolerance is higher in brook stickleback resident to an alkaline lake than those sourced from a neutral lake, a trait that may be related to differences in physiological and transcriptomic responses to alkaline exposure.

physiology↗

bioRxiv2024

Systematic review and meta-analysis of Hyalomma marginatum vertebrate hosts in the EU

Host choice is a determining component of tick population and pathogen transmission dynamics. In Europe, ticks of the genus Hyalomma, which are involved in the transmission of several pathogens such as the Crimean Congo Haemorrhagic fever (CCHF) virus, are suspected to be spreading into new territories where they were previously unreported. Therefore, we performed a systematic review of the tick-host relationship of Hyalomma spp in Europe with a focus on Hyalomma marginatum, combined with a meta-analysis and meta-regression to describe its host preference pattern using three outcome values. Our initial qualitative analysis highlighted an increase in tick-host interaction rate in the last decades mostly in South-eastern and Central Europe. H. marginatum also appeared as the species holding the highest citation rate in terms of its association with hosts, and for which the largest number of host species were reported. The meta-analysis on Hyalomma marginatum host choice revealed preferential interactions for horses in the adult stage and birds of the Emberizidae and Strigidae families, in immature stages. Nevertheless, most of the heterogeneity of tick-host interactions remained unexplained suggesting the involvement of multiple drivers such as environmental or climatic conditions. Our results suggest that H. marginatum is a generalist tick whose distribution depends primarily on environmental conditions such as climate and habitat. Current limitations of our meta-analysis approach to identify hosts preference for H. marginatum and suggestions ways for improvement are further discussed.

ecology↗

bioRxiv2024

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

Ancestral genomes are essential for studying the diversification of life from the last universal common ancestor to modern organisms. Methods have been proposed to infer ancestral gene order, but they lack scalability, limiting the depth to which gene neighborhood evolution can be traced back. We introduce edgeHOG, a tool designed for accurate ancestral gene order inference with linear time complexity. Validated on various benchmarks, edgeHOG was applied to the entire OMA orthology database, encompassing 2,845 extant genomes across all domains of life. This represents the first tree-of-life scale inference, resulting in 1,133 ancestral genomes. In particular, we reconstructed ancestral contigs for the last common ancestor of eukaryotes, dating back around 1.8 billion years, and observed significant functional association among neighboring genes. The method also dates gene adjacencies, revealing conserved histone clusters and rapid sex chromosome rearrangements, enabling computational inference of these features.

evolutionary biology↗

bioRxiv2024

Continuous emergence of phototaxis in Dictyostelium discoideum

The evolutionary transition from uni- to multicellularity is associated with new properties resulting from collective cell behavior. The social amoeba Dictyostelium discoideum alternating between individual cells and multicellular forms of varying size provides a powerful biological system to characterize such emergent properties. Multicellular forms coined slugs have long been described as chemotactic towards cAMP, and also as phototactic. While chemotaxis is also well-documented at the single-cell level, which merely explains slug chemotaxis, we asked whether slug phototaxis is an emergent property of multicellularity. For this, we developed an automated microscopy setup to quantify and compare the migration trajectories of single cells and slugs moving in the dark or illuminated with lateral light. We find that single cells, either extracted from phototactic slugs or taken prior to multicellular aggregation, are not phototactic, implying that slug phototaxis results from interactions between cells that lack this property. Further, by analysing slugs composed of a varying number of cells, we find that phototaxis efficiency increases continuously with slug size. Cell-cell interactions combined with self-organization are thus key elements for this property to emerge.

evolutionary biology↗

bioRxiv2024

Evolution of intrinsic transcriptional terminators in their genomic context

Transcriptional gene expression relies on two fundamental processes - transcription initiation and termination. Transcriptional termination is essential for the coordinated control of gene expression. Intrinsic termination, the major mechanism of transcriptional termination in bacteria, relies on the sequence-dependent folding of nascent mRNA into a hairpin structure that enables RNA polymerase to dissociate from DNA. Despite their central role in regulating expression in prokaryotic genomes, the conservation of intrinsic terminators and the factors that shape their evolution remain poorly understood. Here, we combine comparative genomics with experimental measurements of terminator function, to study the conservation of intrinsic terminators between Escherichia coli and Salmonella enterica subsp. pullorum. While the two species are closely related, the sequence and function of most terminators are not conserved, with less than 20% of all terminators having an identifiable ortholog - in stark contrast to 60% for coding sequences. Terminators with higher sequence conservation also had more conserved function, indicative of stabilizing selection. The local genomic context shapes the evolution of intrinsic terminators, as their sequence conservation is dependent on the conservation of the upstream gene, while their function is affected by the distance to the downstream gene. Ultimately, any theory of gene regulatory network evolution ought to account for how transcriptional terminators evolve.

evolutionary biology↗